No syntax change - NetCDF formats will be automatically recognized.
-Dan
On Tue, Jun 14, 2016 at 3:49 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Thanks Daniel for quick reply.
>
> Has the syntax changed to read the restart files from previous run or I can
> still use -c to read netcdf restart?
>
> -Neha
>
> On 15 June 2016 at 07:34, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> The default restart format has changed in Amber 16 to NetCDF restart,
>> which is an overall better format than the old ASCII format. If you
>> need an ASCII version of your restart you can use cpptraj to create
>> one like so:
>>
>> cpptraj -p solvated.prmtop -y heat.rst -x heat.ascii.rst7
>>
>> -Dan
>>
>> On Tue, Jun 14, 2016 at 3:29 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>> > Dear List,
>> >
>> > I installed AMBER16 recently and compiled the cuda version both parallel
>> > and serial.
>> >
>> > The .out log files look complete but it seems the .rst file has issues
>> > (AMBER16). I think it is in binary format ..there are no coordinates
>> > written to it but the size of the file seems correct. I tried compiling
>> > twice and it didn't give any errors.
>> >
>> > Upon running the same with AMBER14, it outputs coordinates in the right
>> > format in the .rst file.
>> >
>> > Here is the output file with AMBER16
>> >
>> > | PMEMD implementation of SANDER, Release 16
>> >
>> > | Run on 06/15/2016 at 07:07:25
>> >
>> > | Executable path: /home/gandhin/amber16/bin/pmemd.cuda.MPI
>> > | Working directory: /home/gandhin/caroline/pep4
>> > | Hostname: cl2n002
>> >
>> > [-O]verwriting output
>> >
>> > File Assignments:
>> > | MDIN: heat.in
>> >
>> > | MDOUT:
>> > heat.out
>> > | INPCRD:
>> > sys_min.rst
>> > | PARM:
>> > solvated.prmtop
>> > | RESTRT:
>> > heat.rst
>> > | REFC:
>> > sys_min.rst
>> > | MDVEL:
>> > mdvel
>> > | MDEN:
>> > mden
>> > | MDCRD:
>> > mdcrd
>> > | MDINFO:
>> > mdinfo
>> > |LOGFILE:
>> > logfile
>> > | MDFRC:
>> > mdfrc
>> >
>> >
>> > Here is the input file:
>> >
>> > Heating
>> > System
>> > &cntrl
>> >
>> > imin=0,
>> > nmropt=1,
>> > ntx=1,
>> > irest=0,
>> > ntpr=500, ntwr=500, ntwx=500,
>> > iwrap=1,
>> > ntf=2, ntb=1, cut=12.0,
>> > nsnb=20,
>> >
>> > igb=0,
>> > ibelly=0,
>> > ntr=1,
>> > nstlim=250000, nscm=500,
>> > dt=0.002,
>> > ntt=1, temp0=0.0, tempi=0.0,
>> > tautp=0.5
>> >
>> > ntc=2,restraintmask=':1-20',
>> >
>> > restraint_wt=10.0,
>> > &end
>> >
>> >
>> >
>> > &wt type='REST', istep1=0, istep2=0, value1=1.0, value2=1.0,
>> > &end
>> > &wt type='TEMP0', istep1=0, istep2=250000, value1=0.0, value2=293,
>> > &end
>> > &wt type='END'
>> > &end
>> >
>> >
>> > Note: ig = -1. Setting random seed to 545793 based on wallclock time in
>> > microseconds and disabling the synchronization of random numbers
>> > between tasks to improve performance.
>> > | INFO: The nsnb ctrl option does not affect nonbonded list update
>> > frequency.
>> > | It does affect steepest descent minimization freq if ntmin ==
>> 0
>> >
>> > |--------------------- INFORMATION ----------------------
>> > | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
>> > | Version 16.0.0
>> > |
>> > | 02/25/2016
>> > |
>> > | Implementation by:
>> > | Ross C. Walker (SDSC)
>> > | Scott Le Grand (nVIDIA)
>> > |
>> > | Precision model in use:
>> > | [SPFP] - Single Precision Forces, 64-bit Fixed Point
>> > | Accumulation. (Default)
>> > |
>> > |--------------------------------------------------------
>> >
>> > |----------------- CITATION INFORMATION -----------------
>> > |
>> > | When publishing work that utilized the CUDA version
>> > | of AMBER, please cite the following in addition to
>> > | the regular AMBER citations:
>> > |
>> > | - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
>> > | Poole; Scott Le Grand; Ross C. Walker "Routine
>> > | microsecond molecular dynamics simulations with
>> > | AMBER - Part II: Particle Mesh Ewald", J. Chem.
>> > | Theory Comput., 2013, 9 (9), pp3878-3888,
>> > | DOI: 10.1021/ct400314y.
>> > |
>> > | - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
>> > | Duncan Poole; Scott Le Grand; Ross C. Walker
>> > | "Routine microsecond molecular dynamics simulations
>> > | with AMBER - Part I: Generalized Born", J. Chem.
>> > | Theory Comput., 2012, 8 (5), pp1542-1555.
>> > |
>> > | - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
>> > | "SPFP: Speed without compromise - a mixed precision
>> > | model for GPU accelerated molecular dynamics
>> > | simulations.", Comp. Phys. Comm., 2013, 184
>> > | pp374-380, DOI: 10.1016/j.cpc.2012.09.022
>> > |
>> > |--------------------------------------------------------
>> >
>> > |------------------- GPU DEVICE INFO --------------------
>> > |
>> > | Task ID: 0
>> > | CUDA_VISIBLE_DEVICES: 0,1
>> > | CUDA Capable Devices Detected: 2
>> > | CUDA Device ID in use: 0
>> > | CUDA Device Name: Tesla M2090
>> > | CUDA Device Global Mem Size: 5375 MB
>> > | CUDA Device Num Multiprocessors: 16
>> > | CUDA Device Core Freq: 1.30 GHz
>> > |
>> > |
>> > | Task ID: 1
>> > | CUDA_VISIBLE_DEVICES: 0,1
>> > | CUDA Capable Devices Detected: 2
>> > | CUDA Device ID in use: 1
>> > | CUDA Device Name: Tesla M2090
>> > | CUDA Device Global Mem Size: 5375 MB
>> > | CUDA Device Num Multiprocessors: 16
>> > | CUDA Device Core Freq: 1.30 GHz
>> > |
>> > |--------------------------------------------------------
>> >
>> > |---------------- GPU PEER TO PEER INFO -----------------
>> > |
>> > | Peer to Peer support: DISABLED
>> > |
>> > | (Selected GPUs cannot communicate over P2P)
>> > |
>> > |--------------------------------------------------------
>> >
>> >
>> > | Conditional Compilation Defines Used:
>> > | MPI
>> > | PUBFFT
>> > | BINTRAJ
>> > | CUDA
>> > | EMIL
>> >
>> > | Largest sphere to fit in unit cell has radius = 36.851
>> >
>> > | New format PARM file being parsed.
>> > | Version = 1.000 Date = 04/29/16 Time = 14:56:38
>> >
>> > | Note: 1-4 EEL scale factors are being read from the topology file.
>> >
>> > | Note: 1-4 VDW scale factors are being read from the topology file.
>> > | Duplicated 0 dihedrals
>> >
>> > | Duplicated 0 dihedrals
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 1. RESOURCE USE:
>> >
>> --------------------------------------------------------------------------------
>> >
>> > getting new box info from bottom of inpcrd
>> > NATOM = 39632 NTYPES = 20 NBONH = 39470 MBONA = 152
>> > NTHETH = 330 MTHETA = 209 NPHIH = 671 MPHIA = 637
>> > NHPARM = 0 NPARM = 0 NNB = 54069 NRES = 13141
>> > NBONA = 152 NTHETA = 209 NPHIA = 637 NUMBND = 56
>> > NUMANG = 122 NPTRA = 125 NATYP = 34 NPHB = 1
>> > IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
>> > NCOPY = 0
>> >
>> > | Coordinate Index Table dimensions: 10 10 10
>> > | Direct force subcell size = 7.3739 7.3897 7.3701
>> >
>> > BOX TYPE: RECTILINEAR
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 2. CONTROL DATA FOR THE RUN
>> >
>> --------------------------------------------------------------------------------
>> >
>> > default_name
>> >
>> >
>> > General flags:
>> > imin = 0, nmropt = 1
>> >
>> > Nature and format of input:
>> > ntx = 1, irest = 0, ntrx = 1
>> >
>> > Nature and format of output:
>> > ntxo = 2, ntpr = 500, ntrx = 1, ntwr =
>> > 500
>> > iwrap = 1, ntwx = 500, ntwv = 0, ntwe
>> > = 0
>> > ioutfm = 1, ntwprt = 0, idecomp = 0,
>> > rbornstat= 0
>> >
>> > Potential function:
>> > ntf = 2, ntb = 1, igb = 0, nsnb
>> > = 20
>> > ipol = 0, gbsa = 0, iesp = 0
>> > dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
>> >
>> > Frozen or restrained atoms:
>> > ibelly = 0, ntr = 1
>> > restraint_wt = 10.00000
>> >
>> > Molecular dynamics:
>> > nstlim = 250000, nscm = 0, nrespa = 1
>> > t = 0.00000, dt = 0.00200, vlimit = -1.00000
>> >
>> > Berendsen (weak-coupling) temperature regulation:
>> > temp0 = 0.00000, tempi = 0.00000, tautp = 0.50000
>> >
>> > SHAKE:
>> > ntc = 2, jfastw = 0
>> > tol = 0.00001
>> >
>> > NMR refinement options:
>> > iscale = 0, noeskp = 1, ipnlty = 1, mxsub
>> > = 1
>> > scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
>> >
>> > | Intermolecular bonds treatment:
>> > | no_intermolecular_bonds = 1
>> >
>> > | Energy averages sample interval:
>> > | ene_avg_sampling = 500
>> >
>> > Ewald parameters:
>> > verbose = 0, ew_type = 0, nbflag = 1, use_pme
>> > = 1
>> > vdwmeth = 1, eedmeth = 1, netfrc = 1
>> > Box X = 73.739 Box Y = 73.897 Box Z = 73.701
>> > Alpha = 90.000 Beta = 90.000 Gamma = 90.000
>> > NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
>> > Cutoff= 12.000 Tol =0.100E-04
>> > Ewald Coefficient = 0.22664
>> > Interpolation order = 4
>> >
>> > | PMEMD ewald parallel performance parameters:
>> > | block_fft = 0
>> > | fft_blk_y_divisor = 2
>> > | excl_recip = 0
>> > | excl_master = 0
>> > | atm_redist_freq = 320
>> >
>> > LOADING THE CONSTRAINED ATOMS AS GROUPS
>> >
>> >
>> > 5. REFERENCE ATOM COORDINATES
>> >
>> >
>> > default_name
>> >
>> > Mask :1-20; matches 295 atoms
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 3. ATOMIC COORDINATES AND VELOCITIES
>> >
>> --------------------------------------------------------------------------------
>> >
>> > default_name
>> >
>> > begin time read from input coords = 0.000 ps
>> >
>> >
>> >
>> > Begin reading energy term weight changes/NMR restraints
>> > WEIGHT CHANGES:
>> > REST 0 0 1.000000 1.000000 0 0
>> > TEMP0 0 250000 0.000000 293.000000 0 0
>> >
>> > RESTRAINTS:
>> > ** No restraint defined **
>> >
>> > Done reading weight changes/NMR restraints
>> >
>> >
>> >
>> > Number of triangulated 3-point waters found: 13108
>> >
>> > Sum of charges from parm topology file = -0.00000002
>> > Forcing neutrality...
>> >
>> > | Dynamic Memory, Types Used:
>> > | Reals 1820586
>> > | Integers 1441862
>> >
>> > | Nonbonded Pairs Initial Allocation: 12293846
>> >
>> > | GPU memory information (estimate):
>> > | KB of GPU memory in use: 85032
>> > | KB of CPU memory in use: 56682
>> >
>> > | Running AMBER/MPI version on 2 nodes
>> >
>> >
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> > Dr. Neha S. Gandhi,
>> > Vice Chancellor's Research Fellow,
>> > Queensland University of Technology,
>> > 2 George Street, Brisbane, QLD 4000
>> > Australia
>> > LinkedIn
>> > Research Gate
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jun 14 2016 - 15:00:04 PDT
